[gmx-users] distance between two atoms

udi udi_zel at 012.net.il
Sun Nov 22 13:25:04 CET 2009

Hello all Gromacs users,

I'm simulating a 255 a.a peptide which is only a segment of a whole protein.

I'm using the triclinic box with  -d 1.2 nm.

Because the peptide is only a segment out of a larger protein I would like
to restrain the ends of the peptide in order to prevent the peptide 

from closing on its self during the simulation.

I thought to apply distance restraint in order to do so.

Using VMD I measured the distance between the C-alphas of the first and last
a.a. of the peptide and got 88.8A.

I wanted to double check the distance, so I used g_dist and g_mindist and
got a 56A!!! 

I guess that PBC is the reason for the difference.

Which distance (VMD or Gromacs) should I use when applying the distance

Is  such a distance restrain (88.8A) even possible? (too long?)

I would be glad to learn any other way to enforce a minimal movement of  the
ends of the peptide.

Thanks in advance,




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